Marine actinomycete taxon for drug and fermentation product discovery

ABSTRACT

The invention is the discovery of an actinomycete genus, given the name  Salinospora  gen. nov., that displays an obligate requirement of seawater (Na + ) for growth and unique 16S rRNA signature nucleotides. The invention is also the use of the genus for the production and discovery of active biomolecules such as pharmaceutical agents, agrichemicals, immunomodifiers, enzymes and enzyme inhibitors.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation application of U.S. application Ser.No. 11/841,588, filed Aug. 20, 2007, now pending, which is acontinuation application Ser. No. 11/228,416, filed Sep. 15, 2005, nowabandoned, which is a continuation application of U.S. application Ser.No. 09/991,518 filed Nov. 16, 2001, now issued as U.S. Pat. No.7,144,723, which claims the benefit under 35 USC §119(e) to U.S.Application Ser. No. 60/249,356 filed Nov. 16, 2000, now abandoned. Thedisclosure of each of the prior applications is considered part of andis incorporated by reference in the disclosure of this application.

FIELD OF THE INVENTION

The invention relates to the discovery of a novel taxon of marinebacteria of the order Actinomycetales and the use of this taxon for thediscovery and production of proteins, secondary metabolites andbiomolecules for use as pharmaceutical compositions, agrichemicals,immunomodifiers, enzymes and enzyme inhibitors.

BACKGROUND OF THE INVENTION

Microorganisms belonging to the class Actinobacteria, commonly calledactinomycetes, reside taxonomically within the Gram-positive bacteriaand are ubiquitous in terrestrial environments. Actinomycetes are aprolific source of diverse biologically active metabolites. They havebeen a source of a numerous useful products including Pharmaceuticals,agrichemicals, low molecular weight enzyme inhibitors, immunomodifiers,and enzymes for use in a number of industrial applications, from thefood industry to paper making. These microorganisms have also beenuseful in agriculture as a means of pathogen protection and growthenhancement. Although many useful substances have been discovered fromsoil actinomycetes over the last 60 years, the yield of novel productshas drastically decreased as common soil species continually yieldpreviously discovered metabolites. For this reason, there has been amajor effort to discover new actinomycete taxa in the hope that thesemicroorganisms will provide a new source of useful products (Bull etal., 2000).

Actinobacteria are one of a number of classes of bacteria. The classActinobacteria can be further subdivided into six orders, including theActinomycetales which can be broken down into 10 suborders. Classicalmethods for determining taxonomic novelty include morphological andphysiological criteria such as color, presence or absence of mycelia,hyphal branch characteristics, spore pattern and motility, tolerance ofvariation in temperature, salinity and pH, and the ability to utilizevarious substrates. Although these criteria remain an importantcomponent of taxonomic analyses, a new and more definitive method toestablish strain uniqueness is 16S rDNA sequence analysis, which alsoprovides evolutionary information on the isolate (Stackebrandt, et al.,1997).

Membership of a strain within the class Actinobacteria is indicated by16S rDNA sequence similarity values above 80%, as determined bycomparison of almost complete 16S rDNA sequences with the most deeplybranching members of the class, and the presence of signaturenucleotides (Stackebrandt, 1997). Signature nucleotides specific for ataxonomic group are chosen for their presence in more than 95% of themembers of that group. 16S signature nucleotide sequences can be used onvarious taxonomic levels, from defining an order of bacteria to thesubdivision of families into genera. This method provides a powerfulmathematical model of bacterial evolution and an objective, rather thansubjective, set of rules by which bacteria may be assigned a taxonomicstatus within the classification system.

Despite the fact that the oceans cover 70% of the earth's surface, allknown actinomycete genera discovered to date have been land dwellers. Infact, only one marine actinomycete species has been described (Helmkeand Weyland, 1984) and it belongs to a well-known terrestrial genus.Although actinomycetes have been cultured from marine sediments, it iswidely believed that marine isolates are derived from dormantterrestrial spores that were washed into the sea (Goodfellow and Haynes,1984). The “wash-in” theory was postulated because the marine isolatesdid not require seawater for growth, were closely related to terrestrialspecies, and tended to decrease in number with increasing distance fromland (Goodfellow and Williams, 1983). Because many terrestrialactinomycetes can tolerate high salinity and pressure, and because oftheir distribution and physiology, it was concluded that mostactinomycetes have been washed into the sea and collect in sedimentswhere they can survive for long periods of time as spores (Goodfellowand Haynes, 1984). These types of studies have led to the general beliefthat marine actinomycetes are not significantly different from those onland and therefore of little utility as a source of novel industrialproducts.

SUMMARY OF THE INVENTION

The invention is the discovery, isolation and characterization of thefirst major obligate marine actinomycete taxon for which the nameSalinospora gen. nov. is proposed. Members of this genus are readilyrecognized by a series of characteristic features including:

1. Obligate requirement of sodium (seawater) for growth.

2. Presence of at least 4 of the 5 16S rRNA signature nucleotides (Table3) and close phylogenetic relatedness to the Salinospora clade using 16SrRNA treeing methods.

3. Morphological characteristics typically including:

-   -   a.) colony color ranging from orange to brown,    -   b.) no or scant aerial mycelia,    -   c.) diffusable melanin-like pigments and spores that blacken the        colony surface,    -   d.) hyphae that are finely branched and non-fragmenting with        spores produced singly or in clusters.

4. Comparison with a deposit of a type strain CNH646 at the ATCC(American Type Culture Collection; 12301 Parklawn Drive; Rockville, Md.20852) on Sep. 27, 2000 under number ATCC PTA 250 PTA-2501.

The discovery of the Salinospora group refutes prior notions aboutactinomycetes in the marine environment and provides the firstunequivocal evidence that major populations of unique, obligate marineactinomycetes occur widely in ocean sediments. Chemical studies ofSalinospora group members have led to the isolation of novel compoundsand an exceptionally high rate of biologically active extractsindicating that these microorganisms have utility for drug discovery andother industrial applications.

The invention is the use of the novel taxon for the discovery andproduction of proteins, secondary metabolites and other biomolecules foruse in pharmaceutical compositions, agrichemicals, immunomodifiers,enzymes and enzyme inhibitors. Active molecules can be purified from theactinomycetes themselves or metabolites may be purified from the growthmedia. This genus is a rich source of active biomolecules with manydemonstrated pharmacological activities (e.g. antifungal, antimicrobial,anti-cancer). Extracts and products can be used in a number of assayswell known to those skilled in the art to determine the activity of thevarious compounds derived from the actinomycetes.

The invention is the use of the genome of the taxon for the productionof biomolecules in the context of the endogenous actinomycete strain orin other organisms. Genes may be expressed singly or in clusters underthe control of constitutive or inducible promoters. Genes from theinvention may be expressed in heterologous hosts as recombinant or overproducing strains. Other portions of the genome, such as transcriptionalregulatory elements, can also be used in heterologous contexts for thecontrol of transcription. The genome may be either wild-type or mutant.Mutations may be spontaneous or created in a random or site directedmanner by methods well known to those skilled in the art.

The invention is the use of the taxon for the production of geneproducts from heterologous organisms. Genes may be inserted eithersingly or in clusters into the actinomycete strains of the invention forexpression of proteins, secondary metabolties or other biomolecules.Compounds may be isolated from the actinomycetes or the growth media.

The invention is the use of the taxon for pathogen and pest protection,insecticides, herbicides, microbiocides, growth promotion in agricultureand aquaculture applications. Actinomycetes of the instant invention cancompete with harmful micro-organisms in the environment of the plantsproviding a non-toxic means of protecting plants.

BRIEF DESCRIPTION OF THE DRAWINGS

The present invention will be better understood from the followingdetailed description of an exemplary embodiment of the invention, takenin conjunction with the accompanying drawings in which like referencenumerals refer to like parts and in which:

FIG. 1. Structure of salinosporamide A, the first novel, bioactivemetabolite obtained from the Salinospora group. The isolation of thiscompound proves that the Salinospora group is a resource for unique,biologically active metabolites. The producing strain was cultured in aseawater-based medium and the compound was obtained in pure formfollowing a series of chromatographic steps. The structure ofsalinosporamide A was elucidated using 1D and 2D nuclear magneticresonance and high resolution mass spectral data analyses.

FIG. 2. Phylogenetic dendogram created using the neighbor joining methodshowing seven diverse members of the Salinospora clade along withrepresentatives from all genera officially belonging to theMicromonosporaceae family (Koch, et al; 1996). The distance barindicates 1 nucleotide substitution per 100 nucleotides. The Salinosporaclade is shown in the bracket. In parenthesis along side of theSalinospora strain designations are the locations and dates of theexpeditions from which the isolates were obtained. The Salinospora groupto date includes 400-500 isolates that showed the characteristicfeatures 1 and 3 (listed in the Background section). These strains arefrom three expeditions that were grouped first by location and dateobtained, then by morphological diversity within each group. From eachof these sub-groups, isolates were chosen for almost complete 16S rRNAgene sequencing (greater than 95% of the gene). Phylogenetic programscontained in the Phylip and Clustal W packages were used for analysisand the tree was drawn using Treeview 1.6.1.

Applicants made the following biological deposit with the American TypeCulture Collection (ATCC), 10801 University Blvd., Manassas, Va.20110-2209 USA, and International Depositary Authority (IDA) under theterms of the Budapest Treaty on the International Recognition of theDeposit of Microorganisms for the Purposes of Patent Procedure:

Definition: Actinomycete Salinospora, strain CNH646 ATCC No.: PTA-2501Date of Deposit: Sep. 27, 2000 Definition: Actinomycete Salinospora,strain CNB440 ATCC No.: BAA-916 Date of Deposit: Feb. 4, 2004Definition: Actinomycete Salinospora, strain CNB536 ATCC No.: PTA-10582Date of Deposit: Jan. 14, 2010 Definition: Actinomycete Salinospora,strain CNH898 ATCC No.: PTA-5275 (original deposit) Date of Deposit:Jun. 20, 2003 and Definition: Actinomycete Salinospora, strain CNH898ATCC No.: PTA-10583 (second deposit) Date of Deposit: Jan. 14, 2010

DETAILED DESCRIPTION AND PREFERRED EMBODIMENTS

Salinospora strains can be consistently isolated from marine sedimentsand are distinguished by characteristic signature nucleotides, anobligate requirement of seawater (more specifically, Na⁺) for growth,and morphological characteristics. Isolates belonging to this group wereobtained on five separate occasions from tropical to subtropical,near-shore sediments collected from the Atlantic Ocean, the Red Sea andthe Sea of Cortez indicating a world-wide distribution. In thesestudies, a total of 147 independent sediment samples were evaluated and51 of these yielded a total of 182 Salinospora isolates of which sevenwere subjected to in-depth physiological and phylogenetic evaluation(Table 1). Subsequently, over 1000 strains have been obtained fromadditional collections.

Natural location of strains. Select, diverse isolates representing over1000 strains with Salinospora morphology were used for in-depthphylogenetic and physiological analyses. Nearly complete 16S rDNAsequences (>95% of the entire gene) were obtained for all strainslisted. Note that CNB394 and CNB512 are marine-derived Micromonosporaisolates and were carried through analyses to illustrate fundamentaldifferences between Salinospora and Micromonospora genera.

TABLE 1 Year and Habitat descrip. Strain location and depth Genus CNH6431999 Bahamas, Coarse sand, Salinospora Sweetings Cay 1 m CNH646 1999Bahamas, Spur and grove, Salinospora Andros Island 10 m CNH725 2000 RedSea, Coarse sand, Salinospora Sha'b el utal 20 m CNH898 2000 Bahamas,Coarse sand, Salinospora Little San Salvador 30 m CNH964 2000 Sea ofCoarse sand, Salinospora Cortez 30 m Caleta Partida CNB440 1989 Bahamas,Spur and grove, Salinospora Chub Cay 20 m CNB536 1989 Bahamas, Coarsesand and Salinospora Acklins Island seagrass, 10 m CNB394 1989 Bahamas,Coarse sand and Micromonospora Chub Cay seagrass, 1 m CNB512 1989Bahamas, Spur and grove, Micromonospora San Salvador Is. 30 m

All of the 182 Salinospora strains tested failed to grow on an agarmedium when seawater was replaced with deionized water. Sevenphylogenetically diverse strains were further characterized and shown torequire sodium for growth (Table 2), a physiological characteristiccommonly associated with obligate marine bacteria. Sodium requirementshave been studied extensively in Gram-negative marine bacteria and areindicative of highly evolved marine adaptations such as arespiration-dependant sodium ion pump and/or a sodium dependent membranetransport mechanism. The requirement of seawater (sodium) for growth isextremely rare in Gram-positive bacteria and has never before beenreported for an actinomycete with the exception of Rhodococcusmarinonascens (Helmke and Weyland, 1984).

Assay for sodium dependent growth. Physiological growth analysisillustrating fundamental growth differences between Salinospora (inbold) and marine-derived Micromonospora isolates (CNB394, CNB512) areshown in Table 2. Tests were performed on medium M1 which was found tobe optimal for the growth and maintenance of Salinospora andMicromonospora genera. Isolates were screened using a sterile cottonswab to inoculate macerated, vegetative mycelia onto each analyticalmedium which was then incubated at 25-28° C. for six to eight weeks.Growth was checked periodically using a Leica stereoscope at 10-64×magnification. All strains grew equally well in natural seawater (NSW)or artificial seawater (ASW Na+). No detectable growth was observed forany of the Salinospora isolates on M1 prepared with de-ionized water(D1). The two Micromonospora isolates, CNB394 and CNB512, grew better onM1D1 water than on the seawater-based medium. Sodium growth requirementswere tested on M1 prepared with ASW in which all sodium sources werereplaced with equimolar amounts of potassium (M1, ASW K+). The sodiumconcentration in seawater of salinity 35 (used for M1, NSW medium inthis study) is 450 mM. In order to determine the upper limits of sodiumchloride tolerance, strains were tested for growth on M1D1 water inwhich sodium chloride was added to yield final sodium concentrations of600 and 1000 mM. The Salinospora isolates showed no growth at theseelevated sodium levels whereas growth was clearly evident for themarine-derived Micromonospora CNB394 and CNB512.

TABLE 2 Isolates Tested CNB CNB CNB CNB CNB CNH CNH CNH CNH Medium 394512 440 536 643 646 721 898 964 M1, + + ++ ++ ++ ++ ++ ++ ++ NSW M1, ++++ − − − − − − − DI H₂0 M1 + + ++ ++ ++ ++ ++ ++ ++ ASW, Na⁺ M1 + + − −− − − − − ASW K⁺ 600 +/− +/− − − − − − − − mM [Na⁺] 1000 +/− +/− − − − −− − mM [Na⁺]

Salinospora isolates are proving to be a remarkable source ofbiologically active secondary metabolites. Thus far, of the 105 strainsexamined, 86% yielded culture extracts with significant cancer cellcytotoxicity (IC₅₀ values ranging from 0.004-16.4 micrograms/ml againstthe HCT-116 human colon carcinoma cell line). Significant antifungal andantibiotic activities have also been observed from the extracts ofcultures grown under various conditions with 30% yielding MIC values of19.5 micrograms/ml or less against amphotericin resistant Candidaalbicans and 35% yielding extract minimum inhibitory concentration (MIC)values of 25 micrograms/ml or less against vancomycin resistantEnterococcus faecium.

Thin layer chromatography and liquid chromatography/mass spectrometricanalyses, as well as Repetitive Extragenic Palindrome Polymerase ChainReaction (REP-PCR), indicate considerable strain to strain chemical andgenetic diversity. Bioassay-guided fractionation of one active extracthas led to the isolation of a novel series of metabolites that includesa potent cytotoxin (IC₅₀=10 ng/ml against the HCT-116 human coloncarcinoma cell line) that has been named salinosporamide A (FIG. 1).This molecule is most closely related to clasto-lactacystin beta-lactone(also called omuralide), the intermediary hydrolysis product oflactacystin, an anti-microbial product. Salinosporamide A represents thefirst natural product to be discovered that possesses a fusedbeta-lactone gamma-lactam bicyclic ring and is a highly potentanticancer agent.

The Salinospora group was initially recognized after phylogeneticcharacterization of sediment-derived actinomycetes isolated during anexpedition to the Bahamas. Partial 16S rDNA gene sequences from eightmorphologically diverse strains indicated the presence of four signaturenucleotides between positions 198 to 443 of SEQ ID NOs: 3, 4 and 5, ornucleotide positions 207-468 (based on the E. coli 16S rRNA numberingsystem which is well known to those skilled in the art; see also Table 3which utilizes the E. coli 16S rRNA numbering system to compare theSalinospora actinomycetes to those of other Micromonosporaceae genera).These signature nucleotides have subsequently been found in all 45partially sequenced Salinospora strains. Two strains showing the highestphylogenetic diversity (CNH643 and CNH646) were sequenced nearly intheir entirety (GenBank accession numbers AY040619 (SEQ ID NO: 3) andAY040620 (SEQ ID NO: 4), respectively) and found to possess oneadditional signature nucleotide (position 1456) that is alsocharacteristic of this group (Table 3). Phylogenetic analyses of alignedsequences from these strains indicate that they form a distinct andcoherent clade within the Micromonosporaceae (FIG. 2). Signaturenucleotides unify this clade and a high bootstrap value supports clearseparation from the nine currently described genera within the family.SEQ ID NOs: 3 and 4 are identical sequences. SEQ ID NO: 4 is derivedfrom strain CNH646, which was deposited Sep. 27, 2000 (ATCC No.PTA-2501).

16S rRNA signature nucleotides. 16S rRNA signature nucleotides for thegenus Salinospora and all nine currently accepted genera within theMicromonosporaceae are shown in Table 3. Forty-five diverse Salinosporaisolates were partially sequenced and confirmed to have all foursignature nucleotides at positions 207-468. The signature nucleotide atposition 1456 was discovered after subsequent 3′ sequencing of the 16SrRNA gene from several (20) Salinospora isolates. These are originalsignatures observed in this study (in addition to those previouslypublished by Koch et al. 1996) that define the coherence of theSalinospora clade and separate it from other members of the family.Signature nucleotides were aligned to E. coli positions 27-1492 usingall existing members of the Micromonosporaceae in the Ribosomal DatabaseProject. Members of the genus Salinospora show closest homology toMicromonospora olivasterospora (97.1-97.7% similarity), the most deeplyrooted member of that genus, with whom they share eight of 12 previouslypublished signature nucleotide positions. Thus Salinospora strains aremore highly diverged from their closest phylogenetic neighbor than therecently described genus Verrucosispora giformensis which shows 98.0%similarity to Micromonospora olivasterospora and shares 11 of 12previously published signature nucleotides.

TABLE 3 Relative Nucleotide All Other Nucleotide Position of E.Micormonosporaceae Salinospora Positions of SEQ coli 16S rRNA GeneraIsolates ID NOs: 4 and 5 207 (U/C) A 198 366 (A/G) C 351 467 (A/G) U 442468 A U 443 1456 A G 1423

A follow-up study was undertaken in the Bahamas to determine thepersistence of the Salinospora group. From 20 samples collected fromfour transects (0-30 m), 355 actinomycetes were observed and over 90% ofthese displayed characteristic Salinospora morphologies suggesting thatthis group may be the numerically dominant actinomycete in marinesediments. Of those observed, 100 strains were isolated for furtherstudy. The average numbers of Salinospora colony-forming units (cfu's)ranged from 1.2-2.3×10³ cfu's/ml sediment. Over 50% of the Salinosporaisolates appeared on a low nutrient medium (M4) indicating theimportance of using appropriate isolation techniques. Thirteenrepresentatives of eight different colony morphotypes were partiallysequenced and the most phylogenetically diverse isolate (CNH898) wassequenced nearly in its entirety (GenBank Accession number AY040622)(SEQ ID NO: 5). Strain CNH898 was originally deposited on Jun. 30, 2003(ATCC No. PTA-5275) and redeposited on Jan. 14, 2010 (ATCC No.PTA-10583).

An examination of 30 actinomycetes with Salinospora morphologicalcharacteristics that were isolated from the Bahamas in 1989 (Jensen etal, 1991) revealed that all but two of these strains had an obligaterequirement of seawater (Na⁺) for growth. Ten seawater requiring strainsrepresenting six different morphotypes were partially sequenced andfound to possess the five Salinospora signature nucleotides betweenpositions 207-468 (Table 3). The nearly complete 16S rDNA sequence oftwo of these (CNB440 and CNB536, Gen Bank Accession numbers AY040617(SEQ ID NO: 6) and AY040618 (SEQ ID NO: 7), respectively) indicates thatthey are diverse members of the Salinospora clade (FIG. 2). Thus,strains belonging to this new taxon have been isolated from near-shoreBahamian sediments on three separate occasions over an 11-year periodindicating that they are persistent members of the sediment bacterialcommunity.

The two strains that did not require seawater for growth (CNB394 andCNB512) but had colony morphologies similar to Salinospora were found tolack the Salinospora signatures in Table 3. Analyses of the almostcomplete 16S rDNA sequence of these strains showed 99.6-99.9% similarityto Micromonospora aurantiaca str. W2b and the presence of all of thesignature nucleotides previously published for the genus Micromonospora(Koch et al, 1996). The phylogenetic dendogram clearly shows that CNB394and CNB512 are members of the genus Micromonospora (FIG. 2).Micromonospora isolates have been reported from marine sediments(Takizawa et al, 1993), including deep-sea samples (Weyland, 1981),however, unlike Salinospora, this genus is well known from terrestrialsoils and seawater-requiring strains have not been reported.

From extended supra-littoral transects (10 locations, 30 samples) madein the Bahamas (2000 expedition), over 1000 actinomycete colonies wereobserved including low numbers of Micromonosporaceae (ca. 2%), howevernone of these required seawater for growth. The inability to recoverSalinospora strains from supra-littoral samples supports the observationthat these bacteria are restricted to the marine environment.

To determine if Salinospora members had a broader distribution,sediments were collected from the Red Sea and the Sea of Cortez. From 42Red Sea sediment samples, 22 isolates with Salinospora morphologies andan obligate requirement of seawater for growth were obtained. Sixisolates representing 4 major morphotypes were partially sequenced andthe almost complete 16S rDNA sequence of one strain (CNH725, GenBankAccession number AY040621) (SEQ ID NO: 8) is represented in FIG. 3. From36 sediments collected in the Sea of Cortez, 20 seawater-requiringactinomycete strains were isolated and all of these possessedSalinospora morphological characteristics. Eight strains representingfive different morphotypes were partially sequenced and thephylogenetically diverse isolate CNH964 (GenBank Accession numberAY040632 AY040623 (SEQ ID NO: 9)) was sequenced almost in its entirety(FIG. 3). These results clearly indicate that Salinospora members arewidely distributed in marine sediments.

Phylogenetic analyses and physiological characteristics indicate thatthe Salinospora clade represents a new genus within the familyMicromonosporaceae. Although it is unlikely that the diversity withinthis genus has been revealed in the present study, intra-group 16S rDNAsequence similarity (98.6%) and a robust clade topology indicate thatthis genus is comprised of multiple species (FIG. 2). Placement of thegenus Salinospora within the family Micromonosporaceae is supported bythe presence of a complete set of family-specific 16S rDNA signaturenucleotides (Stackelbrandt, 1997).

Despite evidence that actinomycetes can be recovered from deep-oceansediments, only one marine species has been described (Helmke andWeyland, 1984) and the inclusion of this group within the autochthonousmarine microbiota has not been widely accepted (Bull et al., 2000). Ourdata provide the first conclusive evidence for the widespread andpersistent occurrence in marine sediments of unique populations ofobligate marine actinomycetes. Phylogenetic and physiological evidenceindicate that these actinomycetes comprise a new taxon and the genericepithet Salinospora gen. nov. has been proposed. Salinospora strains area prolific source of biologically active secondary metabolites that areuseful for a variety of applications.

Example 1

Sample collection and bacterial isolation. Samples of the top 1 cm ofsediment were collected by SCUBA and processed by either stamping,dilution and heat-shock or both methods. Dilution and heat-shock wascarried out as follows: 1 ml of wet sediment was added to 4 ml ofsterile seawater, heated for six minutes at 55° C., shaken vigorously,and dilutions of 10″² to 10″⁴ were inoculated onto agar media (M1-M4).For stamping, 10 ml of wet sediment were aseptically placed into asterile aluminum dish, dried (ca. 24 hours) in a laminar flow hood,ground lightly with a pestle, pressed into a sterile foam plug (14 mm indiameter) and inoculated onto agar media (M1-M4) by stamping 8-9 timesin a clockwise fashion giving a serial dilution effect. All isolationmedia were prepared with 100% filtered natural seawater. Actinomycetesgenerally appeared after 4-6 weeks of incubation at 25-28° C. and wereconsidered as any colony with a tough leathery texture, dry or foldedappearance and branching filaments with or without aerial mycelia. Allisolation media had final concentrations of 100 micrograms/mlcycloheximide and 5 micrograms/ml rifampicin added after autoclaving.

Media were prepared by methods well known to those skilled in the artand all contain seawater. Recipes for media are as follows: M1: 10 gramsstarch, 4 grams yeast extract, 2 grams peptone, 18 grams agar, 1 liternatural seawater; M2: 6 ml glycerol, 1 gram arginine, 1 gram K₂HPO₄, 0.5grams MgSO₄ 18 grams agar, 1 liter natural seawater; M3: 6 gramsglucose, 2 grams solubilized chitin, 18 grams agar, 1 liter naturalseawater; M4: 2 grams solubilized chitin, 18 grams agar, 1 liter naturalseawater; M5: 18 grams agar, 1 liter natural seawater.

Example 2

DNA purification, amplification, sequencing and phylogenetic analyses.Genomic DNA was prepared as follows: 10 mg of vegetative mycelia grownon M1 agar for 2-4 weeks at 25-28° C. was macerated and an aqueouscleared lysate, created by standard methods, was precipitated with 0.7volumes of isopropanol. The resultant DNA pellet was then washed with70% ethanol and resuspended in 10 mM Tris buffer (pH 8.5) to a finalconcentration of 100 ng/ml. 16S rDNA sequencing templates were amplifiedfrom 10-50 ng of genomic DNA template by the PCR using the primers FC27(5′ AGAGTTTGATCCTGGCTCAG) (SEQ ID NO: 1) and RC1492 (5′TACGGCTACCTTGTTACGACTT) (SEQ ID NO: 2). PCR products were purified witha Qiagen QIAquick PCR clean-up kit using the manufacture's protocols.Partial sequences of morphologically diverse strains were obtained fromnucleotides 80-480 (E. coli numbering system) using the FC27 primer.Select 16S rDNA amplicons were sequenced almost in their entirety onboth top and bottom strands using a total of ten primers. The tencontigs were then assembled yielding gene sequences of 1479 to 1483unambiguous nucleotides. Hypervariable regions in the 16S rDNA sequenceswere excluded yielding a total of 1408 aligned nucleotides. 16S rDNAsimilarity values were calculated by the RDP similarity matrix onlineanalysis and compared to the three nearest neighbors in the RDPdatabase. Sequences were aligned to the secondary structure of membersof the Micromonosporaceae in the RDP (Maidak et al, 2001) using theBioEdit software (Hall, 1999). Phylogenetic analyses were performedusing the neighbor-joining and parsimony based algorithms in the ClustalW software and PHYLIP software packages, respectively (Thompson et al.,1994; Felsenstein, 1993). The dendogram (FIG. 2) was drawn usingTreeview 1.6.1 (Page, 1996).

Example 3

Genetic-analysis by Repetitive Extragenic Palindromic Polymerase ChainReaction (REP-PCR). The genetic diversity of Salinospora strains wasanalyzed using REP-PCR (Versalovic et al., 1991). This technique, whenapplied to the Salinospora group, involves the use of total genomic DNAas a template and PCR primers specific for repetitive sequences presentin the genomes of high G+C content Gram-positive bacteria. The length ofthe PCR products for any one strain will vary with the position of therepetitive sequences in the genome and result in a population ofamplicons of various lengths that when separated on an agarose gelcreate strain-specific banding patterns. This high throughput methodallows for the detection of genetically distinct strains and is moresensitive than 16S rRNA gene analyses as a method to assess geneticdiversity. REP-PCR banding patterns are used to sort strains intodistinct groups that can produce different gene products. Grouping ofstrains based on REP-PCR banding patterns correlate well with groupsbased on the production of secondary metabolites.

Example 4

Production and isolation of useful products. Salinospora strains werecultured in multiple sea-water based media including M1 and CKA (starch5 g, fish hydro-solubles 4 ml, menhaden meal 2 g, kelp powder 2 g,chitosan 2 g, seawater 1 L). An adsorbent resin (XAD-16) was added tothe fermentation 24 hours prior to harvest (day 11). The resin wascollected by filtration, rinsed with deionized water, and eluted withacetone. Alternatively, cells were collected by filtration, freeze driedand extracted with acetone. The extract was concentrated by rotaryevaporation and the residue subjected to C-18 flash chromatographyfollowed by HPLC. The structures of novel fermentation products wereresolved using a variety of methods including one- and two-dimensionalNMR and mass spectroscopy.

Example 5

Antibacterial assay. Extracts from cultured Salinospora strains weretested using standard methods to demonstrate their antibiotic activityagainst Gram-positive and Gram-negative bacteria. The method used totest against Staphylococcus aureus is detailed below. Similar methodsare used to test for antimicrobial activity against other organisms.Extracts were compared to known antibiotics and relative activity levelsdetermined. Extracts with potent antibiotic activity were furtheranalyzed for the presence of novel metabolites.

Briefly, cultures of S. aureus were grown overnight to stationary phase.The number of bacteria per ml was calculated and a uniform number ofbacteria were plated into individual wells containing fresh media.Compounds of interest, including known antibiotic agents (e.g. Oxacillinin DMSO at 0.04 mg/mL), were added to a single row of wells and seriallydiluted down the plate to determine the concentration required to killthe bacteria. Plates were incubated overnight at 37° C. to allow forcell growth. Samples were read in an automated plate reader at 600 nmand MIC concentrations were determined.

Example 6

Antifungal assay. Extracts from cultured Salinospora strains were testedusing standard methods to demonstrate antifungal activity againstCandida albicans. Extracts were compared to known antibiotics and theirrelative activities determined. Extracts with potent antifungal activitywere further analyzed for the presence of novel metabolites.

Briefly, a culture of C. albicans was grown overnight to stationaryphase. The number of cells per ml was calculated and the suspension wasdiluted and added to individual wells of 96-well plates. Alamar blue wasadded to each well as an indicator of viability. Test extracts wereadded to a single row of wells and serially diluted down the plate todetermine the concentration required to kill the fungal cells. Knownantifungal agents such as amphotericin were used as a control. Plateswere incubated for 12-15 hours at 37° C. Cell concentrations weredetermined using an automated plate reader at 600 nm and MICconcentrations were determined.

Example 7

Assay for the inhibition of growth of colon carcinoma cells and ofovarian cancer cells in vitro. The cytotoxicity of extracts from cellsor culture media were assessed in vitro against the human coloncarcinoma cell line HCT116 and the human ovarian carcinoma cell lineA2780 by MTS assay. Cells were plated at 4,000 cells per well in 96 wellmicroliter plates and, after 24 hours, the extract (dissolved in DMSO orother appropriate solvent) was added and serially diluted. The cellswere incubated with the compound at 37° C. for 72 hours, then thetetrazolium dye MTS was added to a final concentration of 333 μg/ml andthe electron coupling agent phenazine methosulfate was added to a finalconcentration of 25 μM. Once reduced, MTS is converted into a waterinsoluble blue crystal formazan and that was read at an absorbance at490 nm with a microplate reader. As dead cells are unable to reduce MTS,the amount of formazan is correlated to the number of viable cells. TheIC₅₀, the drug concentration required to inhibit proliferation of 50% ofthe cells, was used as a measure of efficacy.

Example 8

Anti-Herpes Simplex Virus (HSV-1) assay. Antiviral activity can also bedetermined using an MTS assay. Vero cells were plated into duplicate96-well plates for infection with virus and cytotoxicity control. Oneplate of cells was incubated with virus for an hour at 37° C. Bothplates were overlaid with a series of concentrations of the extract ofinterest and plates were incubated for five days. MTS solution was addedto the plates and the plates were incubated for three hours as describedabove. Absorbance at 490 nm was read with a microplate reader andcorrelated to antiviral activity and cellular toxicity.

Example 9

Chemical mutagenesis of Salinospora strains to generate overproducingstrains. Chemical mutagenesis of Salinospora strains can be performed togenerate strains that overproduce a desired product. For example, astrain that produces an antibiotic at a low level is treated withethylmethylsulfonate (EMS) during the mid-log growth phase. Mutagenizedcultures are streaked onto plates to allow for the isolation ofindividual clones. From the individual clones, cultures are grown andthe antibiotic, in a crude or pure form, is isolated. The relativeyields of the compounds of interest produced by the mutagenized strainsare compared to the original strain to select an overproducing strain.

Example 10

Heterologous gene expression. Actinomycete strains have been useful ashosts for the production of secondary metabolites from other more slowlygrowing organisms (Tang, et al., 2000). Genes, either singly or inclusters, can be expressed in Salinospora strains for the production ofproteins or secondary metabolites. Methods for transferring nucleicacids into bacteria are well known by those skilled in the art.

Example 11

Gene cluster isolation and expression. The synthesis of a number ofactinmycete antibiotics (e.g. actinorhodin, frenolicin, granaticin,griseusin, octatetracycline, and tetracenomycin) are produced byclustered polyketide synthetase (PKS) genes (Hopwood, 1995). PKS genesare classified into two types of large mutifunctional proteins. In PKStype I genes, the substrate progresses through a number of active siteson a single protein. In PKS type II genes, multiprotein complexes areproduced and the substrate progresses from one protein to the next. PKStype II genes have been cloned and expressed in heterologous systems,either in their native groupings or in novel combinations. Combininggenes for the synthesis of secondary metabolites from Salinospora withgenes from other actinomycetes provides a novel method of biologicallyassisted combinatorial chemistry that can lead to the production ofnovel small molecules. Also, Salinospora biosynthetic genes can beshuffled and expressed in an heterologous host leading to the productionof new metabolites. PKS genes are not the only ones that occur inmodules. For example, non-ribosomal peptide synthetases are modular aswell, and are frequently present in the actinomycetes. Biosynthetic geneclusters from the novel Salinospora group can be used as geneticfeedstock for the expression of novel molecules in heterologous strainsor for the overproduction of native and recombinant gene products.

Example 12

Assay for anti-inflammatory activity. Extracts from Salinospora culturesare tested by measuring inhibition of phorbol-induced inflammation(edema) in a mouse ear assays. This is a conventional test which hasbeen accepted as demonstrating a compound's effectiveness in reducinginflammation. The compound is topically applied in acetone to the insidepinnae of the ears of mice in a solution containing an edema-causingirritant, i.e. phorbol 12-myristate 13-acetate (PMA). PMA alone (2microgram per ear) or in combination with varying amounts of the extractis applied to the left ear (5 mice per treatment group) while an acetone(control) is applied to the right. After a 3-hour and 20-minuteincubation at 23° C., the mice are sacrificed, the ears removed, andbores taken and weighed. Edema is measured by subtracting the weight ofthe right ear (control) from the weight of the left ear (treatment). Theresults are recorded as a percent decrease (inhibition) or percentincrease (potentiation) in edema relative to PMA.

Example 13

Enzyme inhibition assay. Extracts from Salinospora strains could betested for their ability to inhibit enzyme activity. Extracts could beprepared as described above and serial dilutions of the extract added toenzyme-substrate mixtures to determine an IC₅₀ for the reaction.

Example 14

Enzyme activity assay. Assays for enzyme activity can be tested bygrowing Salinospora strains in the presence of substrates of interestincluding, but not limited to chitin, lignin, cellulose, and otherrecalcitrant biopolymers, etc. Depending on the substrate, assays can beperformed to determine the amount of substrate remaining or the amountof product produced.

Example 15

Agriculture/aquaculture protection assay. Assays for the protection ofplants from pathogens and general growth enhancement can be performed ina standard greenhouse trial. The strain of interest can be applied tothe plant directly or incorporated into the growth media. Plants couldbe challenged by subjecting them to a pathogen and comparing theirgrowth to control groups treated with a pathogen alone, treated with aSalinospora strain alone, or untreated. Rates of growth could becompared to select for strains with the desired activities.

Although an exemplary embodiment of the invention has been describedabove by way of example only, it will be understood by those skilled inthe field that modifications may be made to the disclosed embodimentwithout departing from the scope of the invention, which is defined bythe appended claims.

A Sequence Listing is attached electronically herewith and uploaded viathe Electronic Filing System of the United States Patent and TrademarkOffice. The entire contents of the Sequence Listing are incorporatedherein by reference. The file details appear as follows:

(a) “UCSD1630-4SEQLIST.txt”-16 Kilobytes

The Sequence Listing, “UCSD1630-4SEQLIST.txt,” was created on Dec. 28,2007 and was uploaded on Dec. 28, 2007.

REFERENCES

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1. A purified compound having the structure of formula I:


2. The compound of claim 1, wherein the compound is isolated from amarine actinomycete of the genus Salinospora.
 3. The compound of claim1, wherein the compound is obtained from a marine actinomycete of thegenus Salinospora.
 4. A pharmaceutical composition comprising apharmaceutically acceptable carrier and a compound having the structureof formula I: